VMD-L Mailing List

From: Joshua Adelman (jla65_at_pitt.edu)
Date: Mon Dec 07 2009 - 06:49:11 CST

Hi Dawn,

You can convert a dcd file to a trr file using catdcd which you can get off of the VMD/NAMD website. Then using trajconv which is a tool distributed with Gromacs, you can convert from a .trr to a .xtc file. There may be other tools that can go directly from .dcd to .xtc, but this is generally what I do.

Josh

On Dec 7, 2009, at 3:43 AM, Dawn wrote:

> Thank you for your response. I will try and hope it works.
> I know Dynamite can do it, but needing xtc file instead of Charmm dcd file. I'll appreciate if you know the transition of dcd to xtc.
> Thank you!
>
> On Sun, Dec 6, 2009 at 11:22 PM, Joshua Adelman <jla65_at_pitt.edu> wrote:
> Hi Dawn,
>
> There is probably a fancy way to do it, but a quick and dirty method that I've used is the following. If you have a series of conformations along the mode, you can have VMD display all frames simultaneously in the 'Trajectory' tab of the Representations GUI. I select the CA atoms and draw them in the VdW representation. Play around with the size of the spheres so that they overlap such that they look like a line or bar along the mode. You can color them by the frame index for clarity. Create another selection where you show the reference structure in whatever representation that you want.
>
> Josh
>
>
> On Dec 6, 2009, at 2:29 PM, Dawn wrote:
>
> > Hi,
> > I want to have porcupine plots for the first principal component PC1(derived from PCA). Would you please tell me if VMD have such function and how to do it?
> >
> > Thanks a lot!
> > Dawn
>
>
>